The Ministry has terminated the tender for the Mine Countermeasure Vessels (MCMVs) and has written a letter to South Korean firm Kangnam Shipyard.
Official sources said Defence Minister Manohar Parrikar signed the recommendation for terminating the tender prior to his departure to Goa yesterday.
The recommendation had been made during the tenure of Arun Jaitley who was in charge of Defence portfolio till early this month.
The Attorney General in his opinion last month said tender conditions have been violated, the sources said.
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India's defence procurement procedure does not allow agents in deals and the government has already encashed Rs 3 crore bank guarantee furnished by Kangnam.
Vendors have to sign a pre-contract integrity pact stating that there will be no middlemen involved.
As per the deal, the South Korean firm was to build two ships while the remaining six were to be manufactured by Goa Shipyard Limited (GSL) under the transfer of technology pact.
Sources said the Defence Acquisition Council, which will meet on Saturday, will decide the next course of action.